NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|996063888|gb|AMK01641|]
View 

ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial [phytoplankton environmental sample]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RuBisCO_large super family cl08232
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 1-126 2.98e-87

Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions.


The actual alignment was detected with superfamily member CHL00040:

Pssm-ID: 471793  Cd Length: 475  Bit Score: 261.18  E-value: 2.98e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063888   1 VGSVIVMIDLVM-GYTAIQSIALWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDP 79
Cdd:CHL00040 260 LGVPIVMHDYLTgGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRMSGGDHIHAGTVVGKLEGER 339

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 996063888  80 LMIKGFYDSLLATNLEVNLPCGIFFEMTWASLRKCMPVASGGIHCGQ 126
Cdd:CHL00040 340 EMTLGFVDLLRDDFIEKDRSRGIYFTQDWVSLPGVLPVASGGIHVWH 386
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-126 2.98e-87

ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit


Pssm-ID: 176981  Cd Length: 475  Bit Score: 261.18  E-value: 2.98e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063888   1 VGSVIVMIDLVM-GYTAIQSIALWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDP 79
Cdd:CHL00040 260 LGVPIVMHDYLTgGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRMSGGDHIHAGTVVGKLEGER 339

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 996063888  80 LMIKGFYDSLLATNLEVNLPCGIFFEMTWASLRKCMPVASGGIHCGQ 126
Cdd:CHL00040 340 EMTLGFVDLLRDDFIEKDRSRGIYFTQDWVSLPGVLPVASGGIHVWH 386
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-126 4.34e-81

Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV , which differ in their taxonomic distribution and subunit composition. Form I is the most abundant class, present in plants, algae, and bacteria, and forms large complexes composed of 8 large and 8 small subunits.


Pssm-ID: 173977  Cd Length: 450  Bit Score: 244.64  E-value: 4.34e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063888   1 VGSVIVMIDLVMGYTAIQSIALWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPL 80
Cdd:cd08212  238 LGSPIIMHDLLTGFTAIQSLAKWCRDNGMLLHLHRAGHATYDRQKNHGIHFRVLAKWLRLSGVDHIHAGTVVGKLEGDPL 317

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 996063888  81 MIKGFYDSLLATNLEVNLPCGIFFEMTWASLRKCMPVASGGIHCGQ 126
Cdd:cd08212  318 VTLGFYDLLRDDYIEKDRSRGIFFTQDWASLPGVMPVASGGIHVGQ 363
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 2-126 1.14e-52

Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of RuBisCO large chain is the catalytic domain adopting a TIM barrel fold.


Pssm-ID: 459631  Cd Length: 292  Bit Score: 167.15  E-value: 1.14e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063888    2 GSVIVMID-LVMGYTAIQSIALWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTV-VGKLEGDP 79
Cdd:pfam00016 107 GGVAVMVDgLVIGPTAITTLRRWFRDNGVILHYHRAGHGAVTRQSKHGISFRVLAKMARLAGADHLHTGTMgVGKLEGDP 186

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 996063888   80 LmikgfyDSLLATNLEVNLPCGIFFEMTWASLRKCMPVASGGIHCGQ 126
Cdd:pfam00016 187 S------DTLRAYMLEEDRARGPFFDQDWGGMPAVMPVASGGIHAGQ 227
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 2-126 3.87e-36

Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate transport and metabolism];


Pssm-ID: 441455  Cd Length: 417  Bit Score: 127.21  E-value: 3.87e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063888   2 GSVIVMID-LVMGYTAIQSIAlwARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPL 80
Cdd:COG1850  240 GANAVMVDvNTVGLSAVQTLR--EEHIGLPIHAHRAGHGAFTRSPLHGISMRVLAKLWRLAGADHLHVGTPVGKMEGDDE 317

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 996063888  81 MIKGFYDSLLAtnlevnlpcgiffemTWASLRKCMPVASGGIHCGQ 126
Cdd:COG1850  318 EVLAIADALLQ---------------PWGGLKPVFPVPSGGQHPGQ 348
 
Name Accession Description Interval E-value
rbcL CHL00040
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
 1-126 2.98e-87

ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit


Pssm-ID: 176981  Cd Length: 475  Bit Score: 261.18  E-value: 2.98e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063888   1 VGSVIVMIDLVM-GYTAIQSIALWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDP 79
Cdd:CHL00040 260 LGVPIVMHDYLTgGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGIHFRVLAKALRMSGGDHIHAGTVVGKLEGER 339

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 996063888  80 LMIKGFYDSLLATNLEVNLPCGIFFEMTWASLRKCMPVASGGIHCGQ 126
Cdd:CHL00040 340 EMTLGFVDLLRDDFIEKDRSRGIYFTQDWVSLPGVLPVASGGIHVWH 386
RuBisCO_large_I cd08212
Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase ...
 1-126 4.34e-81

Ribulose bisphosphate carboxylase large chain, Form I; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV , which differ in their taxonomic distribution and subunit composition. Form I is the most abundant class, present in plants, algae, and bacteria, and forms large complexes composed of 8 large and 8 small subunits.


Pssm-ID: 173977  Cd Length: 450  Bit Score: 244.64  E-value: 4.34e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063888   1 VGSVIVMIDLVMGYTAIQSIALWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPL 80
Cdd:cd08212  238 LGSPIIMHDLLTGFTAIQSLAKWCRDNGMLLHLHRAGHATYDRQKNHGIHFRVLAKWLRLSGVDHIHAGTVVGKLEGDPL 317

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 996063888  81 MIKGFYDSLLATNLEVNLPCGIFFEMTWASLRKCMPVASGGIHCGQ 126
Cdd:cd08212  318 VTLGFYDLLRDDYIEKDRSRGIFFTQDWASLPGVMPVASGGIHVGQ 363
rbcL PRK04208
ribulose bisophosphate carboxylase; Reviewed
 2-126 4.68e-65

ribulose bisophosphate carboxylase; Reviewed


Pssm-ID: 179787  Cd Length: 468  Bit Score: 203.98  E-value: 4.68e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063888   2 GSVIVMIDLVM-GYTAIQSIALWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPL 80
Cdd:PRK04208 254 GSPIVMIDVVTaGWTALQSLREWCRDNGLALHAHRAMHAAFTRNPNHGISFRVLAKLLRLIGVDHLHTGTVVGKLEGDRA 333

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 996063888  81 MIKGFYDSLLATNLEVNLPCGIFFEMTWASLRKCMPVASGGIHCGQ 126
Cdd:PRK04208 334 EVLGYYDILREDFVPEDRSRGIFFDQDWGSIKPVFPVASGGIHPGH 379
RuBisCO_large_I_II_III cd08206
Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate ...
 2-126 5.17e-62

Ribulose bisphosphate carboxylase large chain, Form I,II,III; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubico-like proteins (RLP), are missing critical active site residues.


Pssm-ID: 173971  Cd Length: 414  Bit Score: 194.76  E-value: 5.17e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063888   2 GSVIVMIDLV-MGYTAIQSIALWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPL 80
Cdd:cd08206  226 GSVIVMVDGVtAGWTAIQSARRWCPDNGLALHAHRAGHAAFTRQKNHGISMRVLAKLARLIGVDHIHTGTVVGKLEGDPS 305

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 996063888  81 MIKGFYDSLLATNLEVNLPcGIFFEMTWASLRKCMPVASGGIHCGQ 126
Cdd:cd08206  306 EVKGIADMLREDEVEGDLS-RIFFNQDWGGMKPVFPVASGGLHPGR 350
RuBisCO_large pfam00016
Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of ...
 2-126 1.14e-52

Ribulose bisphosphate carboxylase large chain, catalytic domain; The C-terminal domain of RuBisCO large chain is the catalytic domain adopting a TIM barrel fold.


Pssm-ID: 459631  Cd Length: 292  Bit Score: 167.15  E-value: 1.14e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063888    2 GSVIVMID-LVMGYTAIQSIALWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTV-VGKLEGDP 79
Cdd:pfam00016 107 GGVAVMVDgLVIGPTAITTLRRWFRDNGVILHYHRAGHGAVTRQSKHGISFRVLAKMARLAGADHLHTGTMgVGKLEGDP 186

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 996063888   80 LmikgfyDSLLATNLEVNLPCGIFFEMTWASLRKCMPVASGGIHCGQ 126
Cdd:pfam00016 187 S------DTLRAYMLEEDRARGPFFDQDWGGMPAVMPVASGGIHAGQ 227
RbcL COG1850
Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate ...
 2-126 3.87e-36

Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate transport and metabolism];


Pssm-ID: 441455  Cd Length: 417  Bit Score: 127.21  E-value: 3.87e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063888   2 GSVIVMID-LVMGYTAIQSIAlwARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPL 80
Cdd:COG1850  240 GANAVMVDvNTVGLSAVQTLR--EEHIGLPIHAHRAGHGAFTRSPLHGISMRVLAKLWRLAGADHLHVGTPVGKMEGDDE 317

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 996063888  81 MIKGFYDSLLAtnlevnlpcgiffemTWASLRKCMPVASGGIHCGQ 126
Cdd:COG1850  318 EVLAIADALLQ---------------PWGGLKPVFPVPSGGQHPGQ 348
RuBisCO_large cd08148
Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) ...
 2-125 4.83e-28

Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions.


Pssm-ID: 173969  Cd Length: 366  Bit Score: 105.20  E-value: 4.83e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063888   2 GSVIVMID-LVMGYTAIQSIALwARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPL 80
Cdd:cd08148  220 GANMLMVDvLTAGFSALQALAE-DFEIDLPIHVHRAMHGAVTRSKFHGISMLVLAKLLRMAGGDFIHTGTVVGKMALERE 298

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 996063888  81 MIKGFYDSLlatnlevnlpcgiffEMTWASLRKCMPVASGGIHCG 125
Cdd:cd08148  299 EALGIADAL---------------TDDWAGFKRVFPVASGGIHPG 328
RuBisCO_large_III cd08213
Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase ...
 2-125 7.71e-27

Ribulose bisphosphate carboxylase large chain, Form III; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV , which differ in their taxonomic distribution and subunit composition. Form III is only found in archaea and forms large subunit oligomers (dimers or decamers) that do not include small subunits.


Pssm-ID: 173978  Cd Length: 412  Bit Score: 102.47  E-value: 7.71e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063888   2 GSVIVMIDLVM-GYTAIQSIALWARENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLEGDPL 80
Cdd:cd08213  224 GGKYVMIDVVVaGWSALQYLRDLAEDYGLAIHAHRAMHAAFTRNPRHGISMLVLAKLYRLIGVDQLHIGTAVGKMEGDKE 303

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 996063888  81 MIKGFYDsLLATNLEVNLPCGIFFEMTWASLRKCMPVASGGIHCG 125
Cdd:cd08213  304 EVLRIAD-ILREQKYKPDEEDFHLAQDWGGIKPVFPVASGGLHPG 347
RuBisCO_large_II cd08211
Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase ...
 2-122 5.17e-15

Ribulose bisphosphate carboxylase large chain, Form II; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV , which differ in their taxonomic distribution and subunit composition. Form II is mainly found in bacteria, and forms large subunit oligomers (dimers, tetramers, etc.) that do not include small subunits.


Pssm-ID: 173976  Cd Length: 439  Bit Score: 69.84  E-value: 5.17e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063888   2 GSVIVMID-LVMGYTAIQSialwAREN--DMLLHLHRAGNSTYARQKNH-GTNFRVICKWMRMSGVDHIHAGTV-VGKLE 76
Cdd:cd08211  255 GHVAFLVDgYVAGPAAVTT----ARRRfpDQFLHYHRAGHGAVTSPQSKrGYTAFVLSKMARLQGASGIHTGTMgFGKME 330

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 996063888  77 GDPlmikgfYDSLLATNLEVNLPCGIFFEMTWASLRKCMPVASGGI 122
Cdd:cd08211  331 GES------SDKVIAYMIERDEAQGPLFNQKWYGMKPTTPIISGGM 370
PRK13475 PRK13475
ribulose-bisphosphate carboxylase;
10-122 3.11e-13

ribulose-bisphosphate carboxylase;


Pssm-ID: 184072  Cd Length: 443  Bit Score: 64.74  E-value: 3.11e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063888  10 LVMGYTAIQSIALWAREN--DMLLHLHRAGNSTYARQKN-HGTNFRVICKWMRMSGVDHIHAGTV-VGKLEGDPlmikgf 85
Cdd:PRK13475 261 LVDGYVAGPGAVTTARRQypDQYLHYHRAGHGAVTSPSSkRGYTAFVLSKMARLQGASGIHTGTMgYGKMEGEA------ 334

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 996063888  86 YDSLLATNLEVNLPCGIFFEMTWASLRKCMPVASGGI 122
Cdd:PRK13475 335 DDRVIAYMIERDSAQGPFYHQEWYGMKPTTPIISGGM 371
RuBisCO_IV_RLP cd08205
Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate ...
 2-126 1.08e-08

Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions, like for example 2,3-diketo-5-methylthiopentyl-1-phosphate enolase or 5-methylthio-d-ribulose 1-phosphate isomerase.


Pssm-ID: 173970  Cd Length: 367  Bit Score: 51.77  E-value: 1.08e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063888   2 GSVIVMIDL-VMGYTAIQSIAlwaRENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKLegdpl 80
Cdd:cd08205  223 GANALLINPnLVGLDALRALA---EDPDLPIMAHPAFAGALSRSPDYGSHFLLLGKLMRLAGADAVIFPGPGGRF----- 294

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 996063888  81 mikGF-YDSLLATNLEVNLPcgiffemtWASLRKCMPVASGGIHCGQ 126
Cdd:cd08205  295 ---PFsREECLAIARACRRP--------LGGIKPALPVPSGGMHPGR 330
RLP_NonPhot cd08207
Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose ...
 2-126 2.66e-07

Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions. The specific function of this subgroup is unknown.


Pssm-ID: 173972  Cd Length: 406  Bit Score: 47.69  E-value: 2.66e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996063888   2 GSVIVMIDL-VMGYTAIQSIAlwaRENDMLLHLHRAGNSTYARQKNHGTNFRVICKWMRMSGVDHIHAGTVVGKL-EGDP 79
Cdd:cd08207  236 GGTCVMVSLnSVGLSGLAALR---RHSQLPIHGHRNGWGMLTRSPALGISFQAYQKLWRLAGVDHLHVNGLASKFwESDD 312

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 996063888  80 LMIKGFYDSLlaTNLevnlpcgiffemtWASLRKCMPVASGGIHCGQ 126
Cdd:cd08207  313 SVIESARACL--TPL-------------GGPDDAAMPVFSSGQWGGQ 344
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH